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Questions and answers > RNA structures (DSSR)
Can DSSR detect stacking interaction between ligand and nucleic acid
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lvelve0901:
Hi Xiangjun,
My new target structure is 1F1T from RCSB. It is a malachite green aptamer with a ligand called N,N'-TETRAMETHYL-ROSAMINE (ROS).
If you go to the PDB website and search for this PDB, you can see there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.
http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t
My question is whether DSSR can detect such ligand and RNA interaction?
Here, I also attach the PDB file and json file that I generated for your convenience.
Best,
Honglue
lvelve0901:
Hi Xiangjun,
Also, generally speaking, can DSSR detect protein/peptide and nucleic acid stacking interaction? For example, the stacking between aromatic ring of Phenylalanine and nucleic acid base?
Best,
Honglue
xiangjun:
--- Quote ---there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.
http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t
My question is whether DSSR can detect such ligand and RNA interaction?
--- End quote ---
No, in general. This feature is beyong DSSR’s design scope, at least for now. Why not using the result from reported from the RCSB PDB website? It is an ‘authoritative’ resource, isn't it?
--- Quote ---Also, generally speaking, can DSSR detect protein/peptide and nucleic acid stacking interaction? For example, the stacking between aromatic ring of Phenylalanine and nucleic acid base?
--- End quote ---
You may find SNAP helpful. Again, do not forget the many other resources/tools in the field.
Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
